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Protein and Nucleic acid > STRUCTURE OF NUCLEIC ACIDS > Flashcards

STRUCTURE OF NUCLEIC ACIDS Flashcards

1
Q

Nucleic acids contain only how many monomeric units?

A

4 unique monomeric units

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2
Q

Are more difficult to recognize

A

Distinctive sequences

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3
Q

2 simple tools make NA sequencing
easier than polypeptide sequencing

A

type II restriction endonucleases
gel electrophoresis

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4
Q

Cleave DNA at specific oligonucleotide sites, generating unique fragments of manageable size.

A

Type II

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5
Q

separate NA fragments that differ from one another in length by just a single nucleotide

A

Gel electrophoresis

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6
Q

Chain termination or dideoxy method was invented by?

A

Frederick sanger

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7
Q

It uses enzymatic replication of the DNA to be sequenced

A

Chain termination or dideoxy method

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8
Q

Can be carried out on as little as blank of DNA contained in less than 0.1 microliter

A

1 attomole

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9
Q

Blank detection of the DNA

A

fluorescent

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10
Q

It is more rapid and efficient DNA sequencing technologies

A

Next generation sequencing by Synthesis

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11
Q

Next generation is also known as?

A

(UHT) Ultra-High-Throughput sequencing

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12
Q

Has developed materials and methods allowing manipulation and analysis of extremely small amounts of biomolecules

A

Nanobiotechnology

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13
Q

Blank catalyzes the synthesis of a complementary strand

A

DNA polymerase

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14
Q

DNA polymerase catalyzes the synthesis of a complementary strand

A

Sequencing by Synthesis (SBS)

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15
Q

Have the advantage in that they can directly detect the addition of each base and record that information in digital form for computer analyses

A

Next-gen Sequencers

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16
Q

Hundreds of thousands to hundreds of millions of sequencing reactions can be run at the same time on these instruments

A

Massively Parallel Sequencing

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16
Q

Yielding thousands of Blank of sequence information per run

A

Gigabase

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16
Q

Also contains information that enables quantification of the amount of each DNA molecule within the library.

A

Digital records

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17
Q

The study of the nature and organization of biological information

A

Bioinformatics

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18
Q

Bioinformatics includes blank and blank

A

Functional group and proteomics

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19
Q

Addresses global issues of gene expression
- Provides new insights into evolutionary relationships between organisms.

A

Functional genomics

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20
Q

The study of all the proteins expressed by a certain cell or tissues under specified conditions

A

Proteomics

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21
Q

Polynucleotides strands are inherently Blank

A

Flexible

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22
Q

Double-stranded DNA is a regular blank with H bonds formed between opposing bases on the 2 chains

A

2 chain structure

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23
Q

TRUE OR FALSE
The 2 chains are parallel

A

False (Anti-parallel)

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24
Q

TRUE OR FALSE
The polar sugar-phosphate backbones of the 2 chains are on the inside

A

False (Outside)

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25
Q

Are stacked on the inside of the structure

A

Bases

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26
Q

The DNA has a Blank structure

A

Ladderlike

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27
Q

Base pairs are fixed at Blank apart

A

0.6 nm

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28
Q

This ladderlike structure converts to a blank when given a simple blank

A

double helix, right-handed twist

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29
Q

blank brings the base-pair rungs of the ladder closer together, stacking them blank apart, without affecting the blank distance of 0.6 nm

A

Helical twisting, 0.34 nm, sugar-sugar

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30
Q

This helix repeats itself approximately every blank

A

10 bp

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31
Q

TRUE OR FALSE
Its pitch is 0.34 nm

A

False (3.4 nm)

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32
Q

The major conformation of DNA in solution

A

B-DNA

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33
Q

The base pairing in DNA is size blank

A

Complementary

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34
Q

TRUE OR FALSE
DNA Double helix is an unstable structure

A

False (Stable)

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34
Q

Purines a blank always pair with pyrimidine a blank

A

Large, Small

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35
Q

What makes the DNA Double Helix stable structure?

A

H bonds
Electrostatic interactions
Van der Waals
Hydrophobic interactions

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36
Q

DNA behaves as a blank, flexible molecule

A

Dynamic

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36
Q

TRUE OR FALSE
The Double Helix is not Flexible

A

False (Flexible)

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37
Q

Due to blank DNA is temporarily distort and deform DNA structures over short regions

A

Localized thermal fluctuations

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38
Q

Blank and Blank ensembles of atoms undergo elastic motions on a time scale of nanoseconds (ns)

A

Base and Backbone

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39
Q

These bending influences give the double helix a blank shape

A

roughly spherical

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39
Q

TRUE OR FALSE
The consequences is that the helix bends aggressively

A

False (gently)

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40
Q

Aromatic macrocycles, flat hydrophobic molecules composed of fused, heterocyclic rings.
- Can slip between the stacked base pairs of DNA

A

Intercalating agents

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40
Q

The base pairs move apart to accommodate them, causing a blank of the helix to a more blank structure

A

unwinding, ladderlike

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41
Q

The blank is almost fully extended as successive base pairs are displaced blank from one another

A

Deoxyribose-phosphate, 0.7 nm

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42
Q

The rotational angle about the helix axis between adjacent base pairs is reduced from blank to blank

A

36 degrees to 10 degrees

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42
Q

When duplex DNA molecules are subjected to conditions of pH, temperature, or ionic strength that disrupt base-pairing interactions.

A

Denatured DNA

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43
Q

If temperature is the denaturing agent, the double helix is said to blank

A

melt

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44
Q

Thermal denaturation of DNA can be observed by changes in Blank

A

UV Absorbance

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45
Q
  • Absorbance increase
  • Aromatic bases in DNA interact via their pie-electron clouds when stacked together in the double helix
A

Hyperchromic shift

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45
Q

DNA denaturation can be followed
spectrophotometrically because the
relative absorbance of the DNA
solution at Blank increases as
much as Blank as the bases unstack

A

260 nm, 40%

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46
Q

UV absorbance of the bases is a consequence of blank

A

pie-electron transitions

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46
Q

The midpoint of the absorbance increase

A

melting temperature (Tm)

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47
Q

TRUE OR FALSE
A:T pairs have higher base stacking energies than G:C pairs

A

False (G:C is greater)

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48
Q

Tm is dependent on the Blank of the solution

A

ionic strength

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49
Q

suppress the electrostatic
repulsion between the negatively
charged phosphate groups in the
complementary strands of the
double helix

A

Cations

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50
Q

is the preferred denaturant
because it does not hydrolyze the
glycosidic bonds linking purine bases
to the sugar-phosphate backbone

A

Alkali

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51
Q

the double-stranded form of DNA is
more stable in?

A

Dilute salt solutions

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52
Q

TRUE OR FALSE
denatured DNA will not renature to reform the duplex structure if the denaturing conditions are removed

A

False (it will renature)

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53
Q

the process occurs more quickly if
the temperature is Blank enough to
promote diffusion of the large DNA
molecules but not so warm as to
cause melting

A

warm

53
Q

renaturation which requires reassociation of the DNA strands into a double helix

A

Reannealing

54
Q

TRUE OR FALSE
Renaturation is dependent on both
DNA concentration and time

A

True

55
Q

TRUE OR FALSE
Many of the realignments are perfect

A

False (Imperfect)

56
Q

The blank of DNA is an excellent indicator of the sequence complexity of DNA.

A

Renaturation rate

56
Q

The DNA of bacteriophage T4 contains how many base pairs?

A

2 x 105 base pairs

57
Q

E. coli chromosomes contain how many base pairs?

A

4.64 x 106 base pairs

58
Q

E.coli is considerably more blank in that it encodes more information

A

complex

59
Q

TRUE OR FALSE
It will take shorter for the E.coli DNA strands to find their complementary partners and reanneal

A

False (longer)

60
Q

The rate of DNA duplex formation depends on complementary DNA sequences encountering one another and beginning the process of sequence blank and blank

A

alignment and reannealing

61
Q

different DNA strands of
similar sequence can form?

A

Hybrid Duplexes

62
Q
  • DNA from 2 different species are
    mixed, denatured, and allowed to
    cool slowly so that reannealing can
    occur
  • DNA from one species is similar in
    nucleotide sequence to the DNA of
    the other
A

Hybrid duplexes

62
Q

degree of hybridization is a measure
of the sequence Blank or
blank between the 2 species

A

similarity or relatedness

63
Q

DNA hybrids can be
created Blank if ss-DNA is allowed
to Blank with RNA copies of itself

A

in vitro, anneal

64
Q

about Blank of the DNA from a human form
hybrids with mouse DNA

A

25%

65
Q
  • reveal evolutionary relationships
  • gives researchers the power to
    identify specific genes selectively
    against a vast background of
    irrelevant genetic material
A

NA hybridization

66
Q
  • an appropriately labeled
    oligonucleotide or polynucleotide
  • its sequence is complementary to a
    target gene
  • specifically base pairs with the target
    gene, allowing ID and subsequent
    isolation of the gene
  • assay quantitative expression of genes
    (amount of mRNA synthesized)
A

Probe

67
Q
  • naturally occurring
  • self-replicating
  • extrachromosomal DNA molecules
  • found in bacteria
  • carry genes specifying novel
    metabolic capacities advantageous
    to the host bacterium
A

Plasmids

68
Q
  • in duplex DNA, the two
    strands are wound about
    each other once every
    10 bp, i.e., once every
    turn of the helix
  • ds circular DNA or linear
    DNA duplexes whose
    ends are not free to
    rotate
A

Supercoils

69
Q

more than the normal number of
turns

A

Overwound DNA

70
Q

fewer than the normal number of
turns

A

Underwound DNA

71
Q

How many diameter does the human cell has?

A

20 um

72
Q

How many pairs of ds-DNA molecules in the
form of chromosomes the human cell has?

A

23 pairs

73
Q

average length of human cell

A

= 3 x 109 bp/23 or 1.3
108 nucleotide pairs

74
Q

Blank molecules more than 2 m
of DNA that must be packaged into a
nucleus 10 um in diameter

A

46 dsDNA

75
Q

the DNA must be condensed by a
factor of more than

A

105

76
Q

1st stage of this condensation is
accomplished by neatly wrapping the
DNA around protein spools called

A

nucleosomes

77
Q

are the Fundamental
Structural Unit in Chromatin

A

Nucleosomes

78
Q

the DNA in a eukaryotic cell nucleus
during the interphase between cell
divisions exists as a nucleoprotein
complex → Blank

A

chromatin

79
Q
  • abundant
  • play an important role in chromatin
    structure
A

Histones

79
Q

2 classes of chromatin proteins

A
  • histones
  • nonhistone chromosomal proteins
80
Q
  • a great variety of different proteins
  • involved in genetic regulation;
  • only a few molecules of each per cell
A

nonhistones

81
Q

5 distinct histones

A

H1, H2A, H2B, H3, H4

82
Q

(+)ly charged, Blank and blank that interact via ionic bonds
with the (-)ly charged phosphate
groups on the polynucleotide
backbone

A

arg- or lys-rich proteins

83
Q

a 3-domain protein, organizes an
additional 29–43 bp of DNA and links
consecutive nucleosomes

A

Histone H1

84
Q

each complete nucleosome unit
contains Blank of DNA

A

176–190 bp

85
Q

the N-terminal tails of histones blank and blank are accessible on the surface
of the nucleosome

A

H3 and H4

86
Q

residues in these tails can
be covalently modified

A
  • lys and ser
87
Q

may be
acetylated, methylated, or
ubiquitinated

A

lys

88
Q

may be phosphorylated

A

ser

89
Q

play an important role
in chromatin dynamics and gene
expression

A

modifications

90
Q
  • a single nucleosome and its associated
    H1 linker
A

chromatosome

91
Q

the DNA double helix has a diameter
of about?

A

2 nm

92
Q

the total length of the 46 DNA
molecules in a human cell is roughly

A

2 meters

93
Q

all this DNA must be contained
within the Blank, around 10 mm in
diameter

A

nucleus

94
Q

the first stage in DNA compaction is blank

A

wrapping it around nucleosomes

95
Q

in cells undergoing blank, the
chromatin of each chromosome has
been duplicated and highly
condensed in preparation for
distribution to the 2 daughter cells.

A

mitosis

95
Q

chromosomes are structurally

A

dynamic

96
Q

in the nuclei of Blank (cells
that are not undergoing mitosis), the
chromatin of each chromosome is
dispersed, and despite its flexibility
and limited compaction, it is not
entangled with the chromatin of
other chromosomes

A

interphase cells

97
Q

rich in ds regions that form when
complementary sequences within
the chain come together and join via
Blank base pairing

A

intrastrand

97
Q
  • single-stranded
  • has a much greater number of
    conformational possibilities than
    DNA
A

RNA molecules

98
Q
  • base-paired regions
    loop
  • unpaired regions between base pairs
A

Stem

99
Q

paired regions of RNA cannot form
B-DNA-type double helices because
the Blank are a steric hindrance to this conformation

A

RNA 2’-OH groups

100
Q
  • most prominent 2 structural
    elements in RNA
  • both tRNA and rRNA have large
    amounts of A-form double helix
A

A-form double helices

101
Q

Defined structural motifs recur within
the loops of stem-loop structures

A
  1. U-turns
  2. Tetraloops
  3. Bulges
  4. Junctions
102
Q
  • a loop motif of consensus sequence
    UNRN, N = any nucleotide; R = purine
A

U-turn

103
Q
  • 4-nucleotide loops found at the
    termini of stem-loop structures
A

Tetraloops

104
Q
  • internal loops
  • the RNA strand is forced into a short
    ss loop because one or more bases
    along one strand in an RNA double
    helix finds no base-pairing partners
A

Bulges

105
Q
  • regions where several stemloop
    structures meet
A

Junctions

106
Q

4 basic 2 structural elements in RNA

A
  • stems
  • loops
  • bulges
  • junctions
107
Q

Other 3 structural motifs

A
  • coaxial stacking
  • pseudoknot formation
  • ribose zippers
108
Q
  • the blunt, nonloop ends of
    stemloops situated next to one
    another in the RNA sequence stack
    upon each other to create an
    uninterrupted stack of base pairs
A

coaxial stacking

108
Q

acceptor end of the L-shaped tRNA is formed by
coaxial stacking of the Blank

A

acceptor stem on the TC
stem-loop

109
Q

anticodon end is formed by
coaxial stacking of the
Blank on the anticodon stem-loop

A

dihydrouracil stem-loop

110
Q
  • occur when bases in the
    loops of stem-loop
    structures form a short
    double helix by base
    pairing with nearby ss
    regions in the RNA
A

Pseudoknots

111
Q
  • found when 2 antiparallel, ss regions
    of RNA align as an H-bonded
    network forms between the 2’-OH
    groups of the respective strands, the
    O at the 2’-OH position of one strand
    serving as the H-bond acceptor while
    the H on the 2’-OH of the other
    strand is the H-bond donor
A

ribose zippers

112
Q
  • contain 73 to 94 nucleotides in a single
    chain
  • majority of the bases are H bonded to
    one another
A

tRNA molecules

113
Q

hairpin turns bring Blank of bases in the chain into contact so that double helical regions
form, creating stem-loop 2 structures

A

complementary stretches

114
Q

each cloverleaf consists of Blank—3 loops and the stem where the 3- and 5-ends of the
molecule meet

A

4 basepaired segments

115
Q

4 segments

A
  • acceptor stem
  • D loop
  • anticodon loop
  • TC loop
116
Q

the carboxyl group of an AA is linked
to the 3’-OH of the 3’-terminal A
nucleotide, thus forming an Blank

A

aminoacyl ester

116
Q
  • where the AA is linked to form the
    aminoacyl-tRNA derivative
A

acceptor stem

117
Q

often contains dihydrouridine, or D,
residues

A

D loop

118
Q

unusual bases:

A

inosine, thiouridine,
pseudouridine, hypermethylated
purines

119
Q
  • a double helical segment and 7
    unpaired bases, 3 of which are the
    anticodon
A

anticodon stem-loop

120
Q
  • a 3-nucleotide unit that recognizes
    and base pairs with a particular
    mRNA codon
A

anticodon

121
Q
  • a complementary 3-base unit in
    mRNA providing the genetic info that
    specifies an AA
A

codon

122
Q
  • varies from tRNA to tRNA in the
    number of residues that it has
A

extra or variable loop

123
Q
  • most of the invariant residues
    common to tRNAs lie within the nonH-bonded regions of the cloverleaf
    structure
A

TC stem-loop

124
Q
  • arises from base-pairing
    interactions between
    bases in the D loop with
    bases in the variable
    and TC loops
A

tRNA 3 Structure

124
Q
  • 7 unpaired bases, including the
    sequence T  C ( = Blank)
A

pseudouridine

125
Q

these interactions fold the D and
TC arms together and bend the
cloverleaf into the stable Blank

A

L-shaped 3 form

126
Q

the defining feature of an mRNA is
its Blank

A

primary structure

127
Q
  • nucleotide sequence is translated by
    Blank into a unique AA
    sequence
A

ribosomes

128
Q

mRNA folds back on itself, forming
Blank, as well as more Blank

A

stem-loop 2 structures, complex 3 structures

128
Q

Blank provides the structural
framework of the ribosome

A

rRNA

129
Q

the Blank, whose sequences are not
constrained by the necessity of
encoding a protein, often show
higher orders of structure

A

5′- and 3’-untranslated regions

130
Q

Blank for the small ribosomal
subunit

A

16S rRNA

131
Q
  • Blank is for the large
    ribosomal subunit
A

23S and 5S rRNAs

132
Q

the Blank is a ribozyme

A

23S rRNA

133
Q
  • a large degree of intrastrand sequence
    complementarity is found in all
    ribosomal RNA strands
A

rRNA 2 Structure

134
Q

the loop regions of stem-loops contain

A

U-turns, tetraloops, and bulges

135
Q
  • when ribosomal proteins combine
    with rRNAs and when the ensuing
    ribonucleoprotein complexes, the
    small and large subunits, come
    together to form the complete
    ribosome
A

rRNA 3 Structure

Protein and Nucleic acid (6 decks)

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